Print Syllabus

Syllabus

BK0002 Genome analysis, 15.0 Credits

Genomanalys

Subjects

Bioinformatics Biology Bioinformatic

Education cycle

Master’s level

Modules

Title	Credits	Code
Laboratory project	5.0	0105
Computer exercises	3.0	0106
Group discussions	3.0	0107
Written and oral examination	4.0	0108

Advanced study in the main field

Second cycle, has only first-cycle course/s as entry requirements
Master’s level (A1N)

Grading scale

Language

English

Prior knowledge

- 180 credits at first cycle level, of which

- 60 credits biology, animal science, equine science, veterinary nursing or veterinary medicine

or

- 60 credits agricultural sciences (of which at least 30 credits animal and dairy science/zoology)

and

- English 6

Objectives

The course intends to provide advanced knowledge of methods for studies of eukaryotic genomes, including their organization and evolution. There is a focus on animal genomics, but methodological and theoretical aspects of the course are applicable on many different organisms.

On completion of the course, the student should be able to:

• in detail describe structure, diversity and evolution of eukaryotic genomes and genes,

• in detail describe various types of genetic variation,

• in detail explain state of the art and large-scale methods to analyze genetic variation (eg. whole genome sequencing), and gene expression analysis (eg. RNA-seq),

• apply and critically process basic molecular phylogenetic / -genomic and evolutionary analysis,

• in detail describe the different types of RNA in the transcriptome and their function,

• describe principles for transcriptional regulation,

• describe and plan different approaches for functional analysis of genes and genomes,

• summarize genetic recombination and its applications within genome analysis,

• summarize and evaluate the principles of whole genome mapping and comparative genomics to identify genes and loci underlying mendelian and quantitative inherited diseases as well as important phenotypic traits,

• explain epigenetic and epigenomic markers and methods for the analysis of these,

• explain the concept of genome editing and transgenic animals,

• compile data and apply basic statistics relevant to genome analysis,

• use and evaluate molecular genetic laboratory methods and basic bioinformatics methods.

Content

The course is based on lectures, exercises, discussions and laboratory sessions. The contents build largely on animal genome research. Both laboratory and theoretical teaching is for the most part directly applicable also within eg. human or plant genetics. The course is based on current state-of-the-art methodology and research.

Computer exercises and group discussions will cover:

• molecular evolution and phylogenetics/-genomics,

• genetic variation, sequence analysis and primer design,

• gene mapping and genomewide association analysis,

• QTL analysis,

• whole genome sequencing,

• epigenetics/-genomics,

• copy-number variation analysis

The aim of the computer exercises is to give the students useful tools for basic genetic and genomic analyses. Therefore the computer exercises use free and open source software that the student can download to their own laptop. Apart from in the written and the oral examination, compulsory components occur within eg. exercises, group assignments and laboratory sessions.

In the course the following general skills are trained: oral and written communication, problem solving and critical thinking.

Grading form

The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.

Formats and requirements for examination

Passed written and oral examination. Passed participation in compulsory course modules.

• If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.

• The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.

• If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and who have not yet passed the course.

• For the assessment of an independent project (degree project), the examiner may also allow a student to add supplemental information after the deadline for submission. Read more in the Education Planning and Administration Handbook.

Other information

• The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.

• If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.

Additional information

The course presupposes good prior knowledge of basic genetic mechanisms (genome structure and the genetic code, DNA replication, transcription), RNA processing, translation, regulation of gene expression, general genetics and population genetics, corresponding to 7.5 credits.

Responsible department

Department of Animal Breeding and Genetics